General info:

Working Title: browser window title, favorites: save title
Species name: not required, use "bird" for short notation and not hiding genotypes
Mammal? Bird?
Picture folder: (include http:// for absolute path)
Picture extension: omit "."

* DO NOT USE characters that browsers tend to replace in a url/querystring or are reserved as functional separators, such as: #, ?, &
* Better not use double or trailing characters, like spaces, dots
* DO NOT USE the characters and keywords reserved by this engine as functional separators: _ , ; & MODULE= DATA= &ID=
* If you want to zip/compress your querystring do not use: @ &Z=

To permanently save your data go to Tab SAVE / TEST !

Gene/Locus info:
A gene represents a trait or property of an organism. It is like a switch. The alleles (next tabpage) are the on off positions.

Gene symbol: omit ":"
Gene or locus-name: used in gene overview; not required

 can be used to order phenotype aspects (groups are not labeled), and show multiple pictures per specimen; not required

To permanently save your data go to Tab SAVE / TEST !

Change Order
Note: This is the order on screen; Use allele order to put epistatic genes first...

On screen order (drag to alter):

Allele info:
The alleles are the different forms/mutations of a gene. Decisions are made here about the appearance of the organism.

Gene symbol:
Allele symbol: omit ":", also see tips below

Full effect:
Heterozygous, partial effect: only used if applicable
Epistatics and Wildtype  Wildtype is the default on start-up

NEW: Debug your allele effects with the Testmodule directly - Note: gene and allele data should be somewhat complete !

* The alleles are processed in sequence/order on the whole or per gene as indicated below
* A mutation that blocks other genes entirely like 'albino' should be processed first; "effect is epistatic" can be used to stop processing on the whole
* Per gene the alleles should be in 'order of dominance'; if you want the processing to continue to consider the remaining alleles, you need to implement the alleles as "semi-dominant"
* Use combinations to clean up the phenotype outcome, eg. (het.mutation 1) + (het.mutation 2) = (intermediate phenotype)
* Sometimes you must implement a dominant (or even a multiallelic recessive) gene as "semi-dominant ..."; use different case effect text (eg EFFECT or Effect or effect) to work/differentiate with in a 'combination'
* Recessive is also used for 'split' section in the calculator
* Use ^ for superscript: A^B => AB
* Make sure that superscripts (use ^ ) don't overlap, eg. A^g and A^gl: name them A^g and A^Gl

* [part] and (part) can be ignored in the picture retrieval proces; [part] can also be used as a second language in some calculators
* In some special calculators the pictures can be layered, see here
* Else the name of the picture, that must be uploaded somewhere, should match the name of the color outcome, without spaces, with the correct extension and path (first tabpage)
* Slashes "/" in effect name are not recommended, eg they are used in the url to the picture

To permanently save your data go to Tab SAVE / TEST !

Change Order
Note: Put most dominant alleles of each gene first; Genes with epistatic effects (full albino) first...

Drag alleles to alter intra gene allele order:

Drag genes to order all alleles of the genes (grouped together):

Restore allele order according to gene order (grouped together)

Combinations info:
Use these to fine tune your Outcome descriptions. There is a Testmodule now (tabpage Querystring: Runtime Module).

 can be used to order phenotype aspects (groups are not labeled), and show multiple pictures per specimen; not required
 Words 1: (Exact match)
 Words 2: (Exact match)
 Words 3: (Substitutions)
*: Substitutions are placed at the position of Words 1 or at start of Outcome if Words 1 is empty.
**: Words 1,2,3 are not always required.

NEW: Debug your combinations with the Testmodule directly - Note: gene and allele data should be complete !

* Use combinations to implement epistatic effects other than total white out ... ;-)
* There is a testmodule that can show all substitutions step by step, when things get complex (tabpage Querystring: Runtime Module or "Testmodule" link above); example on next line:
* Use different case and () and [] or - suffix for differentiation of certain effects, eg heterozygous effect; example Horse tobiano/sabino/roan linkage implemented as alleles of one joined gene, having overlapping/redundant effects: Testmodule
* when zipping, Initcap, lowercase and () work best
* New combinations are default applied last; Order is critical in some situations, and can be changed below
* Sometimes leaving a word can reduce the need for more combinations, example: (mutation 1) + (mutation 2) => (mutation 2); note: word(s) 3 left empty here
* Example 'Epistatic combination': Llama calculator => piebald spotted + roan = blue eyed white; requires "special action" at allele level
* Remove words from phenotype can be used for so called 'Enablers', genes that affect others but do not have effects of their own; example:
white shield pied genes in pigeon
* "if outcome is empty ..." can be used as the phenotype when no mutations are present. This way the wildtype/default alleles do not have to be assigned an effect
* Crossing Over can also be used to link genes with unknown distance; just set to 0; and use the appropriate modules of course
* The engine removes excess spaces

To permanently save your data go to Tab SAVE / TEST !

Change Order
Note: Lesser combinations act on preceding combination results also...

Drag combination to alter order:

The querystring, being part of the url, contains the data used by the calculator engine for your species

Runtime Module:  empty to use standard flexmodule and save space in querystring

Querystring length should be well below 2000, current length:

Some browsers can't handle querystring that large. Tips to keep it small:
* Title of calculator or name of gene/locus are not necessary. Keep short or omit.
* You can zip the resulting querystring by means below. Only use that zipped version for publishing though.
* When you zip do not use "@" (or "#" or "&"), trailing "." or spaces, exotic usage of "(" and ")".
* Use initcap words (eg Word) and lowercase (eg word) for use in combinations. Also (Word) and (word) is possible.
* Do not edit the zipped string; publish with the hyperlink to the bottom right
* Always backup the original querystring. Check the zipping function by toggling repeatedly, lengths should be stable in each state (if not send me your data)

Save Querystring to local storage (modern browsers) (backup only)

Compress querystring old method ( BETA, careful with Reload, do not edit; do not use any "@" or "_", publish with hyperlink to the bottom-right ! )
Compress querystring new method ( BETA!, see above; also do not use any trailing ".", publish with hyperlink to the bottom-right ! )
Replace %20 with underscore "_" in Runtime querystring BETA
Compress querystring new shortest method ( Do not use DOuble CApitals or Capital+Numbers) BETA BETA BETA
Last method without splitting on minus sign "-" BETA BETA BETA

Reload with editted querystring (risky)...  |   Reload with editted querystring (safe: new window)...  |   Run (publish) with this querystring (new window)...

 Replace with:
 Try not to replace single characters or reserved words like combination types
  NEVER USE # or ? or & or @

To permanently save your data go to Tab SAVE / TEST !

This Gene overview table will be shown in your runtime calculator:

Gene-info comes here...

(save all "saved" steps beyond session)

The data used by your calculator resides in the querystring/url to your calculator.
To permanently save your data you can add to favorites.
For this you have to make sure that the current data is reflected in the address bar of your browser.
You can use the reload hyperlinks below to do that.
Then you can "add to favorites" in your browser.

Save input: Reload and then manually add to favorites...  |  Save wizard to favorites directly (No reload, IExplorer only)

Save input (new window): Use this link and then manually add to favorites...

Test input or save calculator: Use this link and then manually add to favorites...  |  Save calculator to favorites directly (No reload, IExplorer only)

The "directly" saved favorites use the modules at Henk69's webspace. IExplorer only.

Saved changes this session:
Click hyperlink to revert; opens in an new window/tabpage of your browser

To permanently save your data go to Tab SAVE / TEST !